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Analysis of evolutionary relationships provides new clues to the origins of weedy rice.

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Title: Analysis of evolutionary relationships provides new clues to the origins of weedy rice.
Authors: Han, Bing1 (AUTHOR), Ma, Xiaoding1 (AUTHOR), Cui, Di1 (AUTHOR), Wang, Yanjie1 (AUTHOR), Geng, Leiyue1 (AUTHOR), Cao, Guilan1 (AUTHOR), Zhang, Hui1 (AUTHOR) zhanghui06@caas.cn, Koh, Hee‐Jong2 (AUTHOR) heejkoh@snu.ac.kr, Han, Longzhi1 (AUTHOR) hanlongzhi@caas.cn
Source: Ecology & Evolution (20457758). Jan2020, Vol. 10 Issue 2, p891-900. 10p.
Subject Terms: Rice breeding, Wild rice, Rice, Grain yields, Population of China, Gene ontology, Molecular evolution
Geographic Terms: Jilin Sheng (China), Liaoning Sheng (China), Heilongjiang Sheng (China)
Abstract: Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding. [ABSTRACT FROM AUTHOR]
Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Analysis of evolutionary relationships provides new clues to the origins of weedy rice.
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  Data: <searchLink fieldCode="AR" term="%22Han%2C+Bing%22">Han, Bing</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ma%2C+Xiaoding%22">Ma, Xiaoding</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Cui%2C+Di%22">Cui, Di</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Wang%2C+Yanjie%22">Wang, Yanjie</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Geng%2C+Leiyue%22">Geng, Leiyue</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Cao%2C+Guilan%22">Cao, Guilan</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Zhang%2C+Hui%22">Zhang, Hui</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> zhanghui06@caas.cn</i><br /><searchLink fieldCode="AR" term="%22Koh%2C+Hee‐Jong%22">Koh, Hee‐Jong</searchLink><relatesTo>2</relatesTo> (AUTHOR)<i> heejkoh@snu.ac.kr</i><br /><searchLink fieldCode="AR" term="%22Han%2C+Longzhi%22">Han, Longzhi</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> hanlongzhi@caas.cn</i>
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  Data: <searchLink fieldCode="JN" term="%22Ecology+%26+Evolution+%2820457758%29%22">Ecology & Evolution (20457758)</searchLink>. Jan2020, Vol. 10 Issue 2, p891-900. 10p.
– Name: Subject
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  Data: <searchLink fieldCode="DE" term="%22Rice+breeding%22">Rice breeding</searchLink><br /><searchLink fieldCode="DE" term="%22Wild+rice%22">Wild rice</searchLink><br /><searchLink fieldCode="DE" term="%22Rice%22">Rice</searchLink><br /><searchLink fieldCode="DE" term="%22Grain+yields%22">Grain yields</searchLink><br /><searchLink fieldCode="DE" term="%22Population+of+China%22">Population of China</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+ontology%22">Gene ontology</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+evolution%22">Molecular evolution</searchLink>
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  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Jilin+Sheng+%28China%29%22">Jilin Sheng (China)</searchLink><br /><searchLink fieldCode="DE" term="%22Liaoning+Sheng+%28China%29%22">Liaoning Sheng (China)</searchLink><br /><searchLink fieldCode="DE" term="%22Heilongjiang+Sheng+%28China%29%22">Heilongjiang Sheng (China)</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (He = 0.8386) and can be divided into two groups (japonica‐type and indica‐type). The japonica‐type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica‐types from Jiangsu province (JS) also clustered with the indica‐type landraces from JS province. Comparative transcriptome analysis of WR‚ IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty‐two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
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  Data: <i>Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.1002/ece3.5948
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      – Code: eng
        Text: English
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        PageCount: 10
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    Subjects:
      – SubjectFull: Rice breeding
        Type: general
      – SubjectFull: Wild rice
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      – SubjectFull: Rice
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      – SubjectFull: Grain yields
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      – SubjectFull: Molecular evolution
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      – SubjectFull: Jilin Sheng (China)
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      – SubjectFull: Liaoning Sheng (China)
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      – SubjectFull: Heilongjiang Sheng (China)
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              Text: Jan2020
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